High-throughput screening is an important tool in drug discovery to identify small molecule modulators of biochemical activities. Most assays rely on cumbersome labels, such as fluorophores, antibodies, and radioisotopes that increase costs and can produce high rates of false-positive hits. Label-free formats address many of these limitations, but current approaches often lack the throughput necessary to accommodate large screening campaigns. Here, we present a label-free, high-throughput assay and apply it to analyze key epigenetic and immunological therapeutic targets in oncology. The assay combines Self-Assembled-Monolayers on high-density biochip arrays and matrix assisted laser desorption ionization (MALDI) mass spectrometry, a technique termed SAMDI, that enables rapid and quantitative assays capable of screening hundreds of thousands of compounds per day. The ability to directly visualize and measure the reaction products not only eliminates false positive hits, but also provides a data-rich output that accelerates drug discovery efforts. Taken together, the SAMDI assay opens avenues for faster, more reliable, high-throughput screens for a broad range of biochemical activities.